Recent Developments in Paper-Based Sensors with Instrument-Free Signal Readout Technologies (2020-2023)

Signal readout technologies that do not require any instrument are essential for improving the convenience and availability of paper-based sensors. Thanks to the remarkable progress in material science and nanotechnology, paper-based sensors with instrument-free signal readout have been developed for multiple purposes, such as biomedical detection, environmental pollutant tracking, and food analysis. In this review, the developments in instrument-free signal readout technologies for paper-based sensors from 2020 to 2023 are summarized. The instrument-free signal readout technologies, such as distance-based signal readout technology, counting-based signal readout technology, text-based signal readout technology, as well as other transduction technologies, are briefly introduced, respectively. On the other hand, the applications of paper-based sensors with instrument-free signal readout technologies are summarized, including biomedical analysis, environmental analysis, food analysis, and other applications. Finally, the potential and difficulties associated with the advancement of paper-based sensors without instruments are discussed.

Near-Infrared Fluoride Sensing Nano-Optodes and Distance-Based Hydrogels Containing Aluminum-Phthalocyanine

Fluoride ions are highly relevant in environmental and biological sciences, and there is a very limited number of established fluoride chemical sensors. Previous fluoride-selective optodes were demonstrated with metal-porphyrin as the ionophore and required a chromoionophore for optical signal transduction. We demonstrate here novel optical fluoride sensing with nano-optodes containing an aluminum-phthalocyanine complex (AlClPc) as the single active sensing component, simplifying the conventional ion-selective optodes approach. The fluoride nano-optodes were interrogated in the absorbance and fluorescence modes in the near-infrared region, with absorption around 725 nm and emission peaks at 720 and 800 nm, respectively. The nano-optodes exhibited a lower detection limit around 0.1 μM and good selectivity over a range of common anions including ClO4-, Cl-, Br-, I-, SO42-, NO3-, and AcO-. Furthermore, the nano-optodes were physically entrapped in agarose hydrogels to allow distance-based point-of-care testing (POCT) applications. The 3D networks of the agarose hydrogel were able to filter off large particulates in the samples without stopping fluoride ions to reach the nano-optodes. The fluoride concentrations in real samples including river water, mineral water, and groundwater were successfully determined with the distance-based sensing hydrogel, and the results agreed well with those from commercial fluoride electrodes. Therefore, the results in this work lay the groundwork for the optical detection of fluoride in environmental samples without very sophisticated sample manipulation.

Evaluating Compression-Based Phylogeny Estimation in the Presence of Incomplete Lineage Sorting

This study assesses characteristics of the normalized compression distance (NCD) technique for building phylogenetic trees from molecular data. We examined results from a mammalian biological data set as well as a collection of simulated data with varying levels of incomplete lineage sorting. The implementation of NCD we analyze is a concatenation-based, distance-based, alignment-free, and model-free phylogeny estimation method, which takes concatenated unaligned sequence data as input and outputs a matrix of distances. We compare the NCD phylogeny estimation method with various other methods, including coalescent- and concatenation-based methods.

Microbiome Sample Comparison and Search: From Pair-Wise Calculations to Model-Based Matching

A huge quantity of microbiome samples have been accumulated, and more are yet to come from all niches around the globe. With the accumulation of data, there is an urgent need for comparisons and searches of microbiome samples among thousands of millions of samples in a fast and accurate manner. However, it is a very difficult computational challenge to identify similar samples, as well as identify their likely origins, among such a grand pool of samples from all around the world. Currently, several approaches have already been proposed for such a challenge, based on either distance calculation, unsupervised algorithms, or supervised algorithms. These methods have advantages and disadvantages for the different settings of comparisons and searches, and their results are also drastically different. In this review, we systematically compared distance-based, unsupervised, and supervised methods for microbiome sample comparison and search. Firstly, we assessed their accuracy and efficiency, both in theory and in practice. Then we described the scenarios in which one or multiple methods were applicable for sample searches. Thirdly, we provided several applications for microbiome sample comparisons and searches, and provided suggestions on the choice of methods. Finally, we provided several perspectives for the future development of microbiome sample comparison and search, including deep learning technologies for tracking the sources of microbiome samples.

Paper-Based Device for Naked Eye Urinary Albumin/Creatinine Ratio Evaluation

This paper introduces the concept of "Drawing-PADs" (Drawing paper-based microfluidic analytical devices) allowing to intuitively evaluate the urinary albumin (Alb) index, a clinically important parameter used for the early detection of renal deficiencies related to diabetes, among others. To enable regular monitoring of the Alb index, a simple examination method suitable for self-diagnosis is highly desirable. The Drawing-PADs rely on the simultaneous naked eye detection of Alb and creatinine (Cre) on a single device according to the distance-based microfluidic PAD (μPAD) approach. The Alb index is visualized by simply drawing a straight line connecting the top of two color-changed assay channel sections (Alb and Cre channels), followed by visually confirming the position of the intercept of the drawn straight line. The semiquantitative Alb index evaluation performed with Drawing-PADs does not require any equipment such as a camera, software, or a color reference chart. The obtained results are independent of the sample volume and are not influenced by changes in the absolute Alb and Cre concentrations caused by urine excretion variations, making spot urine assays possible. Classification of Alb index values according to clinically relevant criteria (normoalbuminuria, microalbuminuria, and macroalbuminuria) is readily achieved within 15 min and has been validated for 15 human urine samples including diabetic patients and healthy volunteers.

Distance and Microsphere Aggregation-Based DNA Detection in a Paper-Based Microfluidic Device

In paper-based microfluidics, the simplest devices are colorimetric, giving qualitative results. However, getting quantitative data can be quite a bit more difficult. Distance-based devices provide a user-friendly means of obtaining quantitative data without the need for any additional equipment, simply by using an included ruler or calibrated markings. This article details the development of a quantitative DNA detection device that utilizes the aggregation of polystyrene microspheres to affect the distance that microspheres wick through filter paper. The microspheres are conjugated to single-stranded DNA (ssDNA) oligomers that are partially complementary to a target strand and, in the presence of the target strand, form a three-strand complex, resulting in the formation of aggregates. The higher the concentration of the target strand, the larger the aggregate, and the shorter the distance wicked by the microspheres. This behavior was investigated across a wide range of target concentrations and under different incubation times to understand aggregate formation. The device was then used to successfully detect a target strand spiked in extracted plant DNA.

Distance and Color Change Based Hydrogel Sensor for Visual Quantitative Determination of Buffer Concentrations

We present here an innovative platform for the determination of pH buffer capacity based on FITC-dextran loaded hydrogels. Optical signals from the pH-sensitive hydrogels were analyzed by simple parameters including distance and color change. The methodology was validated on five different buffer systems and exhibited wide linearity (0.1 to 100 mM), good batch-to-batch reproducibility, high versatility, and resistance to background ionic strength changes. Experimental results also fit well with a theoretical model based on numerical simulation. Preliminary application in carbonate alkalinity determination of seawater proved very successful. This hydrogel buffer concentration sensor is fundamentally different from conventional acid-base titrations, brings minimum perturbation to samples, and shows great potential in real applications.

The feasibility of a pragmatic distance-based intervention to increase physical activity in lung cancer survivors

The purpose of this study was to investigate the feasibility and preliminary efficacy of a pragmatic distance-based intervention designed to increase physical activity (PA) participation in lung cancer survivors. Fourteen lung cancer survivors were recruited via invitation from the State Cancer Registry to join a 12-week PA intervention of print materials paired with brief telephone follow-up. Outcome measures of feasibility, PA participation and quality of life (QoL) were assessed at baseline, post-intervention and follow-up via telephone interview. Eligibility, recruitment and attrition rates were 16%, 58% and 29% respectively. No adverse events were reported; however, pain scores worsened following the intervention (median change -3.6, IQR -8.0, 0.0). Average intervention adherence was 91% with low median ratings of participation burden (i.e., all items 1/7) and high trial evaluation (i.e., all items 7/7). Post-intervention, median change in self-reported moderate and vigorous PA was 84 min (IQR -22, 188), and several domains of QoL improved. However, for both of these outcomes, improvements were not maintained at follow-up. Our findings suggest that this pragmatic distance-based intervention was safe, had good adherence rates, and indicate potential for improving short-term PA and QoL in lung cancer survivors. Additional strategies are needed to improve other indicators of feasibility, particularly recruitment, retention and long-term maintenance of improvements. Australian New Zealand Clinical Trials Registration: ACTRN12612000085875.

FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program

FastME provides distance algorithms to infer phylogenies. FastME is based on balanced minimum evolution, which is the very principle of Neighbor Joining (NJ). FastME improves over NJ by performing topological moves using fast, sophisticated algorithms. The first version of FastME only included Nearest Neighbor Interchange. The new 2.0 version also includes Subtree Pruning and Regrafting, while remaining as fast as NJ and providing a number of facilities: Distance estimation for DNA and proteins with various models and options, bootstrapping, and parallel computations. FastME is available using several interfaces: Command-line (to be integrated in pipelines), PHYLIP-like, and a Web server (http://www.atgc-montpellier.fr/fastme/).